Biological Probes to Measure Transcription Dynamics in E. coli

Abstract

RNA molecules exhibit dynamic behaviors that are critical to maintaining normal cell function, and their dynamic nature has been exploited to engineer biological systems. RNA dynamics processes that are often investigated include synthesis, degradation, transport, conformation, localization, and binding. As researchers explore the nature of RNA in increasingly complex ways, it is important that they are equipped with equally complex tools that allow them to interrogate RNA function with fine detail in living systems. Several techniques currently exist to study RNA expression; however, no existing method allows for quantitative measurements of RNA concentration in living cells. As a result, precise characterization of RNA synthesis and degradation with high temporal resolution remains a challenge within the scientific community. This dissertation seeks to demonstrate that a novel technology, fluorescence-activating aptamers, can be used to improve researchers' ability to quantify and to communicate measurements of RNA expression dynamics in both natural and engineered biological systems.